Mercurial > repos > iuc > biom_normalize_table

comparison biom_normalize_table.xml @ 0:a03e97724306 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/biom_format commit f726b353973996a1f59e2044e80ef7c9b75833ab"
author iuc
date Wed, 11 Sep 2019 12:41:04 -0400
parents
children bf72690f0fb0
comparison
equal deleted inserted replaced
-1:000000000000 0:a03e97724306
1 <tool id="biom_normalize_table" name="Normalize" version="@VERSION@.1">
2 <description>a BIOM table</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <expand macro="version_command" />
8 <command detect_errors="exit_code">
9 <![CDATA[
10 biom normalize-table
11 --input-fp '$input_fp'
12 --output-fp '$output_fp'
13 $relative_abund
14 $presence_absence
15 --axis '$axis'
16 ]]>
17 </command>
18 <inputs>
19 <param name="input_fp" argument="--input-fp" type="data" format="biom1" label="BIOM table to normalize" />
20 <param name="relative_abund" argument="--relative-abund" type="boolean" checked="True" truevalue="--relative-abund" falsevalue="" label="Convert table to relative abundance" />
21 <param name="presence_absence" argument="--presence-absence" type="boolean" checked="True" truevalue="--presence-absence" falsevalue="" label="Convert table to presence/absence" />
22 <param argument="--axis" type="select" label="The axis to normalize over">
23 <option value="sample" selected="True">Sample</option>
24 <option value="observation">Observation</option>
25 </param>
26 </inputs>
27 <outputs>
28 <data format="biom1" name="output_fp"/>
29 </outputs>
30 <tests>
31 <test>
32 <param name="input_fp" value="input_abundance_1.biom1" />
33 <param name="relative_abund" value="--relative-abund" />
34 <param name="presence_absence" value="" />
35 <param name="axis" value="sample" />
36 <output name="output_fp" value="normalized_relative_abund_samples.biom" ftype="biom1" compare="sim_size"/>
37 </test>
38 <test>
39 <param name="input_fp" value="input_abundance_1.biom1" />
40 <param name="relative_abund" value="" />
41 <param name="presence_absence" value="--presence-absence" />
42 <param name="axis" value="observation" />
43 <output name="output_fp" value="normalized_presence_absence_observations.biom" ftype="biom1" compare="sim_size"/>
44 </test>
45 </tests>
46 <help><![CDATA[
47 Normalize the values of a BIOM table through various methods. Relative abundance will take the relative abundance of each observation in terms of samples or observations. Presence absensece will convert observations to 1's and 0's based on presence of the observation.
48 ]]></help>
49 <expand macro="citations" />
50 </tool>